October 8, 2020

Greetings!!
Congratulations to the Nobel prize winners in Chemistry : Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of “Genetic scissors: a tool for rewriting the code of life- the CRISPR/Cas9 genetic scissors.” Today’s brief digest covers a wide range of articles on early life microbiome to respiratory microbiome. Happy reading!!!

General microbiome
Electrochemical Investigation of Thiobacillus denitrificans in a Bacterial Composite – Abada et al – Journal of the Electrochemical Society

Pregnancy and early life
Review: Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood – Petersen and Turvey – Current Opinion in Pediatrics

Multi-site human microbiome
Nutritional Targeting of the Microbiome as Potential Therapy for Malnutrition and Chronic Inflammation – Schröder et al – Nutrients

Human respiratory microbiome
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease – Liu et al – bioRxiv

Human gut microbiome
Review: Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation – Xue et al – Animal Nutrition

Ethanol extract of Centella asiatica alleviated dextran sulfate sodium-induced colitis via restoration on mucosa barrier and gut microbiota homeostasis – Li et al – Journal of Ethnopharmacology

Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim – Kazlauskaite et al – bioRxiv

Time-dependent modulation of gut microbiome in response to systemic antifungal agents – Udawatte et al – bioRxiv

Animal microbiome
North American fireflies host low bacterial diversity – Green et al – bioRxiv

Plant, root, and soil microbiome
Anthropogenic Invasion of Micromycetes to Undisturbed Ecosystems of the Larsemann Hills Oasis (East Antarctica) – Vlasov et al – Russian Journal of Biological Invasions

Larch or Mongolian pine? Effects of tree species on soil properties and microbial biomass with the consideration of afforestation time – Teng et al – Ecological Engineering

Water and extremophile microbiome
Understanding the microbial trends in a nitritation reactor fed with primary settled municipal wastewater – Pedrouso et al – Separation and Purification Technology

Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea – Chen et al – Science of The Total Environment

Microbial community structure in the river sediments from upstream of Guanting Reservoir: potential impacts of reclaimed water recharge – Xie et al – Science of The Total Environment

Food microbiology
Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products – Reckem et al – Current Opinion in Food Science

Techniques
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria – Zhang et al – bioRxiv

September 2, 2020

Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!

—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

Clearing up of toxic pollutants using a bacterial protein

A science communication commentary on a recently published paper


Most pollutants are introduced in our environment in the form of herbicides, pesticides, and industrial effluents. The aromatic phenolic compounds, produced by a variety of industries, including phenol-formaldehyde resin, petrochemical plants, coal conversion, and leather processing make up for a major percentage of these pollutants. Improper treatment of these toxic pollutants can lead to heavily contaminated soil and groundwater.

Microorganisms particularly the bacterial species termed as Pseudomonas sp. have been used for a long time to clean up phenol from water in treatment plants. One such (methyl) phenol-degrading strain Pseudomonas putida KCTC 1452 has been studied with respect to its metabolic pathways involved in biodegradation.  The bacterium uses a protein called as DmpR, an acronym for di-methyl phenol regulator, for phenol degradation. While DmpR protein has been used in biosensors for detection of  pollutants in environment, the exact mechanism of DmpR activation has puzzled researchers for many years.

A recent study made a breakthrough by solving the molecular structure of the protein, DmpR when bound to phenol. The challenge was overcome by an international team of researchers from three different countries. Scientists from the Korea Research Institute of Bioscience and Biotechnology (KRIBB), South Korea worked together with scientists from the Kavli Institute of Nanoscience Delft, Netherlands and the Department of Molecular Biology, Umea University, Sweden to understand the mechanism of DmpR by solving its phenol-bound crystal structure. This study published in Nature Communications, provides valuable insights into the oligomerization and the signal transduction mechanism of DmpR, which eventually results in degradation of phenolic pollutants.

The team led by Dr. Eui Jeon Woo at the Disease Target Structure Research Center, KRIBB and  Dr. Chirlmin Joo at the Department of Bionanoscience, at the Kavli Institute pioneered the DmpR structural studies advancing the DmpR biosensor technology field. Their discovery of the tetrameric oligomerization state, in contrast to previously thought hexameric state, of the protein helped in understanding its binding to signal transduction factors. The researchers also discovered that protein itself does not utilize energy from hydrolysis of ATP, the cellular currency, to attain oligomeric state but rather directs the energy towards signal transduction and transcriptional activation of proteins involved in the (methyl)phenol-degradative system. With a better understanding of this protein structure and function, highly sensitive whole-cell biosensors can be engineered which can sense and degrade these toxic pollutants. Such sensors can help to prevent accumulation of toxic chemicals that could otherwise cause serious ecological damage as well as contaminate food supplies.  Similarly, DmpR related proteins could also be developed as biosensors that can be used to test different pollutant levels present in the water bodies for protection of the aquatic flora and fauna, thus helping towards preserving ecological niches.

Citation: Park, K., Kim, S., Lee, S. et al. Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR. Nat Commun 11, 2728 (2020). https://doi.org/10.1038/s41467-020-16562-5


Arti Dumbrepatil is a science writer. She did her postdoctoral work at the University of Michigan, Ann Arbor, MI, USA. During her tenure at the University of Michigan, she has worked as a Science Communication Fellow (at the Natural History Museum, UMICH) and as a Science Communication Writer (LSA, UMICH). Arti continues to write as a contributing science writer to American Society for Biochemistry and Molecular Biology (ASBMB),Microbiome Digest,Bio Voice News.

Twitter @rtisciwrites

May 1, 2020

Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY

March 23, 2020

In today’s digest, review on biliary tract microbiome, effect of disinfection on water microbiome, resveratrol on adipose tissue browning via gut microbiome modelling and influence of livestock farm environment on human gut microbiota and antibiotic resistome.

Hope all readers are staying safe at home!

General microbiome

Intestinal microbiota and its association with colon cancer and red/processed meat consumption – Nadine Abu‐Ghazaleh – Journal of Gastroenterology and Hepatology

Is it time to consider gut microbiome readouts for precision diagnosis and treatment of alcoholic liver disease? – Gail A.M. Cresci – Hepatology

Biliary tract microbiota: a new kid on the block of liver diseases? – Nicoletti A – European Review for Medical and Pharmacological Sciences

Human microbiome

Characteristics of the urinary microbiome in kidney stone patients with hypertension – Fengping Liu – Journal of Translational Medicine

Pregnancy associates with alterations to the host and microbial proteome in vaginal mucosa – Christina Farr Zuend – American Journal of Reproductive Immunology

Prebiotics inhibit proteolysis by gut bacteria in a host diet-dependent manner: a three stage continuous in vitro gut model experiment – Xuedan Wang – Applied and Environmental Microbiology

Animal experiments

Resveratrol enhances brown adipose tissue activity and white adipose tissue browning in part by regulating bile acid metabolism via gut microbiota remodeling – Suocheng Hui – International Journal of Obesity

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms – Jian Sun – Nature Communications

Effects of the dietary fibre inulin and Trichuris suis products on inflammatory responses in lipopolysaccharide-stimulated macrophages – Laura J. Myhill – Molecular Immunology

Deoxycholic Acid-Induced Gut Dysbiosis Disrupts Bile Acid Enterohepatic Circulation and Promotes Intestinal Inflammation – Mengque Xu – Digestive Diseases and Sciences

Commensal Bacteria Impact a Protozoan’s Integration into Murine Gut Microbiota in a Dietary Nutrient-dependent Manner – Applied and Environmental Microbiology

Plant, root and soil microbiome

Rhizosphere fungal communities of wild and cultivated soybeans grown in three different soil suspensions – Chunling Chang – Applied Soil Ecology

Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions – Ning Wang – FEMS Microbial Ecology

Water microbiome

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard – Sławomir Sułowicz – Science of the Total Environment

Disinfection exhibits systematic impacts on the drinking water microbiome – Zihan Dai – Microbiome

Microbial diversity in deep subsurface hot brines of the North West Poland: from a community structure to isolate characteristics – Agnieszka Kalwasińska – Applied and Environmental Microbiology

Non microbiology picks

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs – Sangeun Jeon – BioRxiv

Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model – Barry Rockx – BioRxiv

September 30, 2019

Monday morning digest covers exciting updates in microbiome with – meta analysis on role of probiotics in human depression , stool banking guidelines for fecal microbiota transplant, expert view on translation of gut microbiome to clinics and a historical peek into use of ceramic baby milk bottles in prehistoric times. Enjoy reading!

General microbiome

Translating the gut microbiome: ready for the clinic? – Susan V. Lynch – Nature Reviews Gatroenterology and Hepatology

Uterine immunity and microbiota: A shifting paradigm – Chiara Agostinis – Frontiers in Immunology

Human microbiome

Cigarette smoking and oral microbiota in low-income and African-American populations – Yaohua Yang – Journal of Epidemiology and Community Health

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut

Animal experiments

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3 – Zheng Kuang – Science

Transfusional iron overload and intravenous iron infusions modify the mouse gut microbiota similarly to dietary iron – Francesca La Carpia – Biofilms and Microbiomes

Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production – Jonathan Breton – Nutrition

Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut – Ulla Hynönen – Anaerobe

Intestinal inflammation increases convulsant activity and reduces antiepileptic drug efficacy in a mouse model of epilepsy – Carmen De Caro – Scientific Reports

The fecal resistome of dairy cattle is associated with diet during nursing – Jinxin Liu – Nature Communications

Neohesperidin Prevents Colorectal Tumorigenesis by Altering the Gut Microbiota – Yanling Gong – Pharmacological Research

Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass – Jiao Wu – Nutrition

Plant, root, soil microbiome

A bioinformatics guide to plant microbiome analysis – Rares Lucaciu – Frontiers in Plant Science

Beyond pathogens: microbiota interactions with the plant immune system – Paulo José PL Teixeira – Current Opinion in Microbiology

Water microbiome

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea‐land transition – Esther Molina-Menor – Microbial Biotechnology

Probiotics

Bacillus coagulans R11 maintained intestinal villus health and decreased intestinal injury in lead-exposed mice by regulating the intestinal microbiota and influenced the function of faecal microRNAs – Si-Cheng Xing – Environmental Pollution

Effect of probiotics on depressive symptoms: A meta-analysis of human studies – Kah Kheng Goh – Psychiatry Research

Non Microbiology Picks

Milk of ruminants in ceramic baby bottles from prehistoric child graves – J. Dunne – Nature

 

September 24, 2019

Today’s digest is about diet-microbiota interactions in personalized  nutrition, interesting story on single bacterium association with fatty liver disease and how the gut microbiota adapt to red meat consumption.

General microbiome

Diet–microbiota interactions and personalized nutrition – Aleksandra A. Kolodziejczyk – Nature Reviews Microbiology

Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism – Caroline Mullineaux-Sanders – Nature Reviews Microbiology

The interaction between the gut Microbiota and herbal medicines – Xuedong An – Biomedicine & Pharmacotherapy

Gut microbiota: what is its place in pharmacology? – Aleksandra Tarasiuk – Expert Review of Clinical Pharmacology

Human microbiome

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae – Jing Yuan – Cell Metabolism

Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission – Fabienne Humbel – Clinical Gastroenterology and Hepatology

Butyrate‐Producing Gut Bacteria and Viral Infections in Kidney Transplant Recipients: A Pilot Study – John R. Lee – Transplant Infectious Disease

Metabolomics and Microbial Composition Increase Insight into the Impact of Dietary Differences in Cirrhosis – I. Jane Cox – Liver International

Animal experiments

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates – Livia S. Zaramela – Nature Microbiology

A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota – Weijun Wang – Scientific Reports

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids – Florencia Correa-Fiz – Scientific Reports

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko- Applied and Environmental Microbiology

Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats – Lin-Xiu Guo – Pharamacological Research

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota – Motoko Koyama – Immunity

Metformin Alters the Duodenal Microbiome and Decreases the Incidence of Pancreatic Ductal Adenocarcinoma Promoted by Diet-induced Obesity – Tien S Dong – American Journal of Physiology

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach – Maria Guirro – PlosOne

Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling – Cristina Torres-Fuentes – Faseb Journal

Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice – Wang Zhang – Biomedicine & Pharmacotherapy

Plant, root, soil microbiome

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil – Hualing Hu – Chemosphere

Phyllosphere colonisation by a soil Streptomyces sp. promotes plant defense responses against fungal infection – Sophie Vergnes – Molecular Plant-Microbe Interactions

Water microbiome 

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea – Wirulda Pootakham – Microbiology Open

Probiotics
Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri – Casey A. Chamberlain – PlosOne

Probiotic Bifidobacterium bifidum G9‐1 ameliorates phytohemagglutinin‐induced diarrhea caused by intestinal dysbiosis -Yutaka Makizaki – Microbiology and Immunology

May 31, 2019

Happy Friday!! Today’s digest contains reviews on the role of microbiota in immune memory formation and bioinformatic tools for soil microbiome analysis

General microbiome

*Review: The microbiome and immune memory formation – Kathy D. McCoy – Immunology and Cell biology

Preprint – Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing – Emily Crawford – bioRxiv

Animal experiments

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes) – Sébastien Duperron – Environmental Science & Technology Letters

Plant, root, and soil microbiome

*Book chapter : Bioinformatics Tools for Soil Microbiome Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Belowground Microbial Communities: Key Players for Soil and Environmental Sustainability – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

Book chapter: Single-Cell Genomics and Metagenomics for Microbial Diversity Analysis – Rama Kant Dubey – Part of the SpringerBriefs in Environmental Science book series

In vitro digestion and fermentation of three polysaccharide fractions from Laminaria japonica and their impact on lipid metabolism-associated human gut microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Preprint – Biogeographical patterns in soil bacterial communities across the Arctic region – Lucie A Malard – bioRxiv

Water and extremophile microbiome

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient – Marie Simonin – Environmental Microbiology

Phages and viruses

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages – Jakub Barylski – Systematic Biology

Techniques

Protocol: Analysis of Microbial Siderophores by Mass Spectrometry – Tomas Pluhacek – Part of the Methods in Molecular Biology

Review: A guide to visualizing the spatial epigenome with super‐resolution microscopy – Jianquan Xu – The FEBS Journal

March 14, 2019

Today’s digest covers interesting reviews on microbiota for immunotherapies, non-digestible carbohydrates for infant microbiota and contribution of marine microbiota in reactive oxygen species; research articles on how gluten sensitivity is affected by duodenal microbiota and how ginger intake affects mouse microbiota.

General microbiome

Review: Mining the microbiota for microbial and metabolite-based immunotherapies – Ashwin N. Skelly – Nature Reviews Immunology

Pregnancy and early life microbiome

Relationship between vitamin D status and the vaginal microbiome during pregnancy – Kimberly K. Jefferson – Journal of Perinatology

Review: Shaping the Infant Microbiome With Non-Digestible Carbohydrates – Stella A. Verkhnyatskaya – Frontiers in Microbiology

Variations in early gut microbiome are associated with childhood eczema – Yu Zhang – FEMS Microbiology Letters

Human gut microbiome

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction – Meera K. Shenoy – Microbiome

Effects of bowel preparation on the human gut microbiome and metabolome – Naoyoshi Nagata – Scientific Reports

Human colon mucosal biofilms from healthy or colon cancer hosts are carcinogenic – Sarah Tomkovich – The Journal of Clinical Investigation

Animal experiments

Host NLRP6 exacerbates graft-versus-host disease independent of gut microbial composition – Tomomi Toubai – Nature Microbiology

Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2 – Alberto Caminero – Nature Communications

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline – Mahdi Ghanbari – Scientific Reports

Beneficial effects of ginger on prevention of obesity through modulation of gut microbiota in mice – Jing Wang – European Journal of Nutrition

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats – Melisa Crawford – Lipids

Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders – Elisabetta Mondo – BioRxiv

The gut microbiota regulates mouse biliary regenerative responses – Wenli Liu – BioRxiv

Plant, root, soil microbiome

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems – Maria J. Mosqueira – Scientific Reports

Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments – Adam J. Kessler – Nature Microbiology

Effects of graphene oxide and graphite on soil bacterial and fungal diversity – Christian Forstner – BioRxiv

Water microbiome and extremophiles

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Non-microbiology picks

Nano-bot can probe inside human cells – Science Daily